PCR and real-time PCR primers developed for detection and identification of Bifidobacterium thermophilum in faeces

BACKGROUND: Culture-independent methods based on the 16S ribosomal RNA molecule are nowadays widely used for assessment of the composition of the intestinal microbiota, in relation to host health or probiotic efficacy. Because Bifidobacterium thermophilum was only recently isolated from human faeces until now, no specific real-time PCR (qPCR) assay has been developed for detection of this species as component of the bifidobacterial community of the human intestinal flora. RESULTS: Design of specific primers and probe was achieved based on comparison of 108 published bifidobacterial 16S rDNA sequences with the recently published sequence of the human faecal isolate B. thermophilum RBL67. Specificity of the primer was tested in silico by similarity search against the sequence database and confirmed experimentally by PCR amplification on 17 Bifidobacterium strains, representing 12 different species, and two Lactobacillus strains. The qPCR assay developed was linear for B. thermophilum RBL67 DNA quantities ranging from 0.02 ng/microl to 200 ng/microl and showed a detection limit of 10(5) cells per gram faeces. The application of this new qPCR assay allowed to detect the presence of B. thermophilum in one sample from a 6-month old breast-fed baby among 17 human faecal samples tested. Additionally, the specific qPCR primers in combination with selective plating experiments led to the isolation of F9K9, a faecal isolate from a 4-month old breast-fed baby. The 16S rDNA sequence of this isolate is 99.93% similar to that of B. thermophilum RBL67 and confirmed the applicability of the new qPCR assay in faecal samples. CONCLUSION: A new B. thermophilum-specific qPCR assay was developed based on species-specific target nucleotides in the 16S rDNA. It can be used to further characterize the composition of the bifidobacterial community in the human gastrointestinal tract. Until recently, B. thermophilum was considered as a species of animal origin, but here we confirm with the application of this new PCR assay the presence of B. thermophilum strains in the human gut.

Designed ankyrin repeat proteins: a new approach to mimic complex antigens for diagnostic purposes?

Inhibitory antibodies directed against coagulation factor VIII (FVIII) can be found in patients with acquired and congenital hemophilia A. Such FVIII-inhibiting antibodies are routinely detected by the functional Bethesda Assay. However, this assay has a low sensitivity and shows a high inter-laboratory variability. Another method to detect antibodies recognizing FVIII is ELISA, but this test does not allow the distinction between inhibitory and non-inhibitory antibodies. Therefore, we aimed at replacing the intricate antigen FVIII by Designed Ankyrin Repeat Proteins (DARPins) mimicking the epitopes of FVIII inhibitors. As a model we used the well-described inhibitory human monoclonal anti-FVIII antibody, Bo2C11, for the selection on DARPin libraries. Two DARPins were selected binding to the antigen-binding site of Bo2C11, which mimic thus a functional epitope on FVIII. These DARPins inhibited the binding of the antibody to its antigen and restored FVIII activity as determined in the Bethesda assay. Furthermore, the specific DARPins were able to recognize the target antibody in human plasma and could therefore be used to test for the presence of Bo2C11-like antibodies in a large set of hemophilia A patients. These data suggest, that our approach might be used to isolate epitopes from different sets of anti-FVIII antibodies in order to develop an ELISA-based screening assay allowing the distinction of inhibitory and non-inhibitory anti-FVIII antibodies according to their antibody signatures.

Tn6198, a novel transposon containing the trimethoprim resistance gene dfrG embedded into a Tn916 element in Listeria monocytogenes

OBJECTIVES: To characterize Tn6198, a novel conjugative transposon from the clinical Listeria monocytogenes strain TTH-2007, which contains the tetracycline and trimethoprim resistance genes tet(M) and dfrG, respectively, and to assess its transferability in vitro and in situ. METHODS: The complete sequence of Tn6198 was determined using a primer walking strategy. Horizontal gene transfer studies were performed by filter matings, as well as on the surface of smear-ripened cheese and smoked salmon. The presence of Tn916-like circular intermediates was determined by PCR. Antibiotic resistance was determined by the broth microdilution method and microarray hybridization. RESULTS: Sequencing of Tn6198 revealed that a 3.3 kb fragment containing dfrG was integrated between open reading frames 23 and 24 of Tn916. Furthermore, an additional copy of Tn916 was present in L. monocytogenes TTH-2007. Both elements were transferred simultaneously and separately in vitro to recipients L. monocytogenes 10403S and Enterococcus faecalis JH2-2 by conjugation, resulting in either tetracycline- and trimethoprim-resistant or solely tetracycline-resistant transconjugants. On the surface of cheese and salmon, only L. monocytogenes 10403S transconjugants were detected. CONCLUSIONS: This study reports the first Tn916-like element associated with a trimethoprim resistance gene, as well as the first fully characterized transposon conferring multidrug resistance in L. monocytogenes. This is of concern, as trimethoprim is administered to listeriosis patients with β-lactam allergy and as Tn6198 has a large potential for dissemination, indicated by both intra-species and inter-genus transfer.

Advances in Kartvelian Morphology and Syntax. Contributions to the festival of languages Bremen, 17 Sep to 7 Oct, 2009

Within the scope of Festival of Languages took place in 2009 the Conference Advances in Kartvelian Morphology and Syntax. Selected presentations are presented in this publication. The authors discuss topics such as anaphora in Svan, intonation in Georgien, pragmatics of subordinating clauses in Georgian, but also research on modern developments as SMS-communication in Georgian language area etc. DEUTSCH: Im Rahmen des Festivals der Sprachen fand im Jahre 2009 an der Universität Bremen die Tagung Advances in Kartvelian Morphology and Syntax statt. Ausgewählte Vorträge werden mit dieser Publikation vorgestellt. Die Autoren behandeln unter anderem Themen wie Ana-pher im Svanischen, Intonation im Georgischen, Pragmatik von Nebensätzen des Georgi-schen, aber auch Forschungen über moderne Entwicklungen wie die SMS-Kommunikation im georgischsprachigen Sprachraum usw. CONTENTS: NINO AMIRIDZE, TAMAR RESECK & MANANA TOPADZE GÄUMANN: Preface; KEVIN TUITE: The Kartvelian suffixal intransitive; MANANA KOBAIDZE: Towards the morphological and syntactical classification of Georgian verbs; RENÉ LACROIX: Origin of Sets I–II suffixes in South Caucasian through reanalysis; STAVROS SKOPETEAS & CAROLINE FÉRY: Prosodic cues for exhaustive interpretations: a production study on Georgian intonation; WINFRIED BOEDER: Anaphora in Svan; YASUHIRO KOJIMA : The position of rom and the pragmatics of subordinate clauses in Georgian; NATIA AMAGHLOBELI : Morphological aspects of Georgian SMS language.

Boron-Bearing Kornerupine from Fiskenaesset, West Greenland: A Reexamination of Specimens from the Type Locality

In 1884, Lorenzen proposed the formula MgAI2SiO6 for his new mineral kornerupine from Fiskenæsset and did not suspect it to contain boron. Lacroix and de Gramont (1919) reported boron in Fiskenæsset kornerupine, while Herd (1973) found none. New analyses (ion microprobe mass analyser and spectrophotometric) of kornerupine in three specimens from the type locality, including the specimens analysed by Lorenzen and Herd, indicate the presence of boron in all three, in amounts ranging from 0.50 to 1.44 wt.% B203, e.g. (Li0.04 Na0.01 Ca0.01) (Mg3.49 Mn0.01 Fe0.17 Ti0.01 Al5.64)Σ9.30 (Si3.67 Al1.02 B0.31)Σ5 O21 (OH0.99 F0.01) for Lorenzen's specimen. Textures and chemical compositions suggest that kornerupine crystallized in equilibrium in the following assemblages, all with anorthite (An 92-95) and phlogopite (XFe = atomic Fe/(Fe + Mg) = 0.028-0.035): (1) kornerupine (0.045)-gedrite (0.067); (2) kornerupine (0.038-0.050)-sapphirine (0.032-0.035); and (3) kornerupine (0.050)-hornblende. Fluorine contents of kornerupine range from 0.01 to 0.06%, of phlogopite, from 0.09 to 0.10%. In the first assemblage, sapphirine (0.040) and corundum are enclosed in radiating bundles of kornerupine; additionally sapphirine, corundum, and/or gedrite occur with chlorite and pinite (cordierite?) as breakdown products of kornerupine. Kornerupine may have formed by reactions such as: gedrite + sapphirine + corundum + B203 (in solution) + H20 = kornerupine + anorthite + Na-phlogopite under conditions of the granulite facies. Boron for kornerupine formation was most likely remobilized by hydrous fluids from metasedimentary rocks occurring along the upper contact of the Fiskenæsset gabbro-anorthosite complex with amphibolite.

Acute muscular sarcocystosis: an international investigation among ill travelers returning from tioman island, malaysia, 2011-2012.

BACKGROUND Through 2 international traveler-focused surveillance networks (GeoSentinel and TropNet), we identified and investigated a large outbreak of acute muscular sarcocystosis (AMS), a rarely reported zoonosis caused by a protozoan parasite of the genus Sarcocystis, associated with travel to Tioman Island, Malaysia, during 2011-2012. METHODS Clinicians reporting patients with suspected AMS to GeoSentinel submitted demographic, clinical, itinerary, and exposure data. We defined a probable case as travel to Tioman Island after 1 March 2011, eosinophilia (>5%), clinical or laboratory-supported myositis, and negative trichinellosis serology. Case confirmation required histologic observation of sarcocysts or isolation of Sarcocystis species DNA from muscle biopsy. RESULTS Sixty-eight patients met the case definition (62 probable and 6 confirmed). All but 2 resided in Europe; all were tourists and traveled mostly during the summer months. The most frequent symptoms reported were myalgia (100%), fatigue (91%), fever (82%), headache (59%), and arthralgia (29%); onset clustered during 2 distinct periods: "early" during the second and "late" during the sixth week after departure from the island. Blood eosinophilia and elevated serum creatinine phosphokinase (CPK) levels were observed beginning during the fifth week after departure. Sarcocystis nesbitti DNA was recovered from 1 muscle biopsy. CONCLUSIONS Clinicians evaluating travelers returning ill from Malaysia with myalgia, with or without fever, should consider AMS, noting the apparent biphasic aspect of the disease, the later onset of elevated CPK and eosinophilia, and the possibility for relapses. The exact source of infection among travelers to Tioman Island remains unclear but needs to be determined to prevent future illnesses.

Neutrophils mediate blood-spinal cord barrier disruption in demyelinating neuroinflammatory diseases

Disruption of the blood-brain and blood-spinal cord barriers (BBB and BSCB, respectively) and immune cell infiltration are early pathophysiological hallmarks of multiple sclerosis (MS), its animal model experimental autoimmune encephalomyelitis (EAE), and neuromyelitis optica (NMO). However, their contribution to disease initiation and development remains unclear. In this study, we induced EAE in lys-eGFP-ki mice and performed single, nonterminal intravital imaging to investigate BSCB permeability simultaneously with the kinetics of GFP(+) myeloid cell infiltration. We observed a loss in BSCB integrity within a day of disease onset, which paralleled the infiltration of GFP(+) cells into the CNS and lasted for ∼4 d. Neutrophils accounted for a significant proportion of the circulating and CNS-infiltrating myeloid cells during the preclinical phase of EAE, and their depletion delayed the onset and reduced the severity of EAE while maintaining BSCB integrity. We also show that neutrophils collected from the blood or bone marrow of EAE mice transmigrate more efficiently than do neutrophils of naive animals in a BBB cell culture model. Moreover, using intravital videomicroscopy, we demonstrate that the IL-1R type 1 governs the firm adhesion of neutrophils to the inflamed spinal cord vasculature. Finally, immunostaining of postmortem CNS material obtained from an acutely ill multiple sclerosis patient and two neuromyelitis optica patients revealed instances of infiltrated neutrophils associated with regions of BBB or BSCB leakage. Taken together, our data provide evidence that neutrophils are involved in the initial events that take place during EAE and that they are intimately linked with the status of the BBB/BSCB.

A cysteine protease inhibitor of plasmodium berghei is essential for exo-erythrocytic development

Plasmodium parasites express a potent inhibitor of cysteine proteases (ICP) throughout their life cycle. To analyze the role of ICP in different life cycle stages, we generated a stage-specific knockout of the Plasmodium berghei ICP (PbICP). Excision of the pbicb gene occurred in infective sporozoites and resulted in impaired sporozoite invasion of hepatocytes, despite residual PbICP protein being detectable in sporozoites. The vast majority of these parasites invading a cultured hepatocyte cell line did not develop to mature liver stages, but the few that successfully developed hepatic merozoites were able to initiate a blood stage infection in mice. These blood stage parasites, now completely lacking PbICP, exhibited an attenuated phenotype but were able to infect mosquitoes and develop to the oocyst stage. However, PbICP-negative sporozoites liberated from oocysts exhibited defective motility and invaded mosquito salivary glands in low numbers. They were also unable to invade hepatocytes, confirming that control of cysteine protease activity is of critical importance for sporozoites. Importantly, transfection of PbICP-knockout parasites with a pbicp-gfp construct fully reversed these defects. Taken together, in P. berghei this inhibitor of the ICP family is essential for sporozoite motility but also appears to play a role during parasite development in hepatocytes and erythrocytes.

Telomerase inhibitors based on quadruplex ligands selected by a fluorescence assay

The reactivation of telomerase activity in most cancer cells supports the concept that telomerase is a relevant target in oncology, and telomerase inhibitors have been proposed as new potential anticancer agents. The telomeric G-rich single-stranded DNA can adopt in vitro an intramolecular quadruplex structure, which has been shown to inhibit telomerase activity. We used a fluorescence assay to identify molecules that stabilize G-quadruplexes. Intramolecular folding of an oligonucleotide with four repeats of the human telomeric sequence into a G-quadruplex structure led to fluorescence excitation energy transfer between a donor (fluorescein) and an acceptor (tetramethylrhodamine) covalently attached to the 5′ and 3′ ends of the oligonucleotide, respectively. The melting of the G-quadruplex was monitored in the presence of putative G-quadruplex-binding molecules by measuring the fluorescence emission of the donor. A series of compounds (pentacyclic crescent-shaped dibenzophenanthroline derivatives) was shown to increase the melting temperature of the G-quadruplex by 2–20°C at 1 μM dye concentration. This increase in Tm value was well correlated with an increase in the efficiency of telomerase inhibition in vitro. The best telomerase inhibitor showed an IC50 value of 28 nM in a standard telomerase repeat amplification protocol assay. Fluorescence energy transfer can thus be used to reveal the formation of four-stranded DNA structures, and its stabilization by quadruplex-binding agents, in an effort to discover new potent telomerase inhibitors.

Mammalian mad2 and bub1/bubR1 recognize distinct spindle-attachment and kinetochore-tension checkpoints

Metaphase checkpoint controls sense abnormalities of chromosome alignment during mitosis and prevent progression to anaphase until proper alignment has been attained. A number of proteins, including mad2, bub1, and bubR1, have been implicated in the metaphase checkpoint control in mammalian cells. Metaphase checkpoints have been shown, in various systems, to read loss of either spindle tension or microtubule attachment at the kinetochore. Characteristically, HeLa cells arrest in metaphase in response to low levels of microtubule inhibitors that leave an intact spindle and a metaphase plate. Here we show that the arrest induced by nanomolar vinblastine correlates with loss of tension at the kinetochore, and that in response the checkpoint proteins bub1 and bubR1 are recruited to the kinetochore but mad2 is not. mad2 remains competent to respond and is recruited at higher drug doses that disrupt spindle association with the kinetochores. Further, although mad2 forms a complex with cdc20, it does not associate with bub1 or bubR1. We conclude that mammalian bub1/bubR1 and mad2 operate as elements of distinct pathways sensing tension and attachment, respectively.

Tetraploid State Induces p53-dependent Arrest of Nontransformed Mammalian Cells in G1

A “spindle assembly” checkpoint has been described that arrests cells in G1 following inappropriate exit from mitosis in the presence of microtubule inhibitors. We have here addressed the question of whether the resulting tetraploid state itself, rather than failure of spindle function or induction of spindle damage, acts as a checkpoint to arrest cells in G1. Dihydrocytochalasin B induces cleavage failure in cells where spindle function and chromatid segregation are both normal. Notably, we show here that nontransformed REF-52 cells arrest indefinitely in tetraploid G1 following cleavage failure. The spindle assembly checkpoint and the tetraploidization checkpoint that we describe here are likely to be equivalent. Both involve arrest in G1 with inactive cdk2 kinase, hypophosphorylated retinoblastoma protein, and elevated levels of p21WAF1 and cyclin E. Furthermore, both require p53. We show that failure to arrest in G1 following tetraploidization rapidly results in aneuploidy. Similar tetraploid G1 arrest results have been obtained with mouse NIH3T3 and human IMR-90 cells. Thus, we propose that a general checkpoint control acts in G1 to recognize tetraploid cells and induce their arrest and thereby prevents the propagation of errors of late mitosis and the generation of aneuploidy. As such, the tetraploidy checkpoint may be a critical activity of p53 in its role of ensuring genomic integrity.

MEDLINEplus: building and maintaining the National Library of Medicine's consumer health Web service

MEDLINEplus is a Web-based consumer health information resource, made available by the National Library of Medicine (NLM). MEDLINEplus has been designed to provide consumers with a well-organized, selective Web site facilitating access to reliable full-text health information. In addition to full-text resources, MEDLINEplus directs consumers to dictionaries, organizations, directories, libraries, and clearinghouses for answers to health questions. For each health topic, MEDLINEplus includes a preformulated MEDLINE search created by librarians. The site has been designed to match consumer language to medical terminology. NLM has used advances in database and Web technologies to build and maintain MEDLINEplus, allowing health sciences librarians to contribute remotely to the resource. This article describes the development and implementation of MEDLINEplus, its supporting technology, and plans for future development.

Spectroscopie Raman de fibres électrofilées : développement de méthodes et application aux fibres individuelles

L’électrofilage est une technique de mise en œuvre efficace et versatile qui permet la production de fibres continues d’un diamètre typique de quelques centaines de nanomètres à partir de l’application d’un haut voltage sur une solution concentrée de polymères enchevêtrés. L’évaporation extrêmement rapide du solvant et les forces d’élongation impliquées dans la formation de ces fibres leur confèrent des propriétés hors du commun et très intéressantes pour plusieurs types d’applications, mais dont on commence seulement à effleurer la surface. À cause de leur petite taille, ces matériaux ont longtemps été étudiés uniquement sous forme d’amas de milliers de fibres avec les techniques conventionnelles telles que la spectroscopie infrarouge ou la diffraction des rayons X. Nos connaissances de leur comportement proviennent donc toujours de la convolution des propriétés de l’amas de fibres et des caractéristiques spécifiques de chacune des fibres qui le compose. Les études récentes à l’échelle de la fibre individuelle ont mis en lumière des comportements inhabituels, particulièrement l’augmentation exponentielle du module avec la réduction du diamètre. L’orientation et, de manière plus générale, la structure moléculaire des fibres sont susceptibles d’être à l'origine de ces propriétés, mais d’une manière encore incomprise. L’établissement de relations structure/propriétés claires et l’identification des paramètres qui les influencent représentent des défis d’importance capitale en vue de tirer profit des caractéristiques très particulières des fibres électrofilées. Pour ce faire, il est nécessaire de développer des méthodes plus accessibles et permettant des analyses structurales rapides et approfondies sur une grande quantité de fibres individuelles présentant une large gamme de diamètre. Dans cette thèse, la spectroscopie Raman confocale est utilisée pour l’étude des caractéristiques structurales, telles que l’orientation moléculaire, la cristallinité et le désenchevêtrement, de fibres électrofilées individuelles. En premier lieu, une nouvelle méthodologie de quantification de l’orientation moléculaire par spectroscopie Raman est développée théoriquement dans le but de réduire la complexité expérimentale de la mesure, d’étendre la gamme de matériaux pour lesquels ces analyses sont possibles et d’éliminer les risques d’erreurs par rapport à la méthode conventionnelle. La validité et la portée de cette nouvelle méthode, appelée MPD, est ensuite démontrée expérimentalement. Par la suite, une méthodologie efficace permettant l’étude de caractéristiques structurales à l’échelle de la fibre individuelle par spectroscopie Raman est présentée en utilisant le poly(éthylène téréphtalate) comme système modèle. Les limites de la technique sont exposées et des stratégies expérimentales pour les contourner sont mises de l’avant. Les résultats révèlent une grande variabilité de l'orientation et de la conformation d'une fibre à l'autre, alors que le taux de cristallinité demeure systématiquement faible, démontrant l'importance et la pertinence des études statistiques de fibres individuelles. La présence de chaînes montrant un degré d’enchevêtrement plus faible dans les fibres électrofilées que dans la masse est ensuite démontrée expérimentalement pour la première fois par spectroscopie infrarouge sur des amas de fibres de polystyrène. Les conditions d'électrofilage favorisant ce phénomène structural, qui est soupçonné d’influencer grandement les propriétés des fibres, sont identifiées. Finalement, l’ensemble des méthodologies développées sont appliquées sur des fibres individuelles de polystyrène pour l’étude approfondie de l’orientation et du désenchevêtrement sur une large gamme de diamètres et pour une grande quantité de fibres. Cette dernière étude permet l’établissement de la première relation structure/propriétés de ces matériaux, à l’échelle individuelle, en montrant clairement le lien entre l’orientation moléculaire, le désenchevêtrement et le module d'élasticité des fibres.

Environmental Degradation, Climate Change and Migration: from Research to Policy-Making. IES Policy Brief Issue 2013/08/September 2013

Summary. In recent months, the migratory impacts of environmental degradation and climate change have gained increased worldwide attention. In response to the publication of the EC Staff Working Document on Climate Change, Environmental Degradation and Migration, this policy brief critically outlines current themes and issues that surround this global phenomenon, specifically the findings of current international research which frame the discussions on terminology and current legal, political and institutional conceptual debates. Several proposals were put forward during a Policy Forum in January 2013. Firstly, there is a need for tailored and actionable research outputs that take into account political pressures and realities on the ground. Secondly, migration and climate policies would be clearly boosted through the elaboration of a common policy-oriented research agenda of which elements were put forward at the event. Finally, efficient communication tools and channels could be developed to transfer research findings to policy-makers.